PubMedication: do you get your best ideas in the Pub? CC-BY-ND image via trombone65 on Flickr.

Many people claim they get all their best ideas in the pub, but for lots of scientists their best ideas probably come from PubMed.gov – the NCBI’s monster database of biomedical literature. Consequently, the database has spawned a whole slew of tools that riff off the PubMed name, with many puns and portmanteaus (aka “PubManteaus”), and the pub-based wordplays are very common. [1,2]

All of this might make you wonder, are there any decent PubMed puns left? Here’s an incomplete collection:

PubCrawlerpubcrawler.ie “goes to the library while you go to the pub…” [3,4]

PubChasepubchase.com is a “life sciences and medical literature recommendations engine. Search smarter, organize, and discover the articles most important to you.” [5]

PubFig nothing to do with PubMed, but research done on face and image recognition that happens to be indexed by PubMed. [7]

PubGetpubget.com is a “comprehensive source for science PDFs, including everything you’d find in Medline.” [8]

PubLons publons.comOK, not much to do with PubMed directly but PubLons helps you “you record, showcase, and verify all your peer review activity.”

PubMine “supports intelligent knowledge discovery” [9]

PubNetpubnet.gersteinlab.org is a “web-based tool that extracts several types of relationships returned by PubMed queries and maps them into networks” aka a publication network graph utility. [10]

GastroPub repackages and re-sells ordinary PubMed content disguised as high-end luxury data at a higher premium, similar to a Gastropub.

PubQuiz is either the new name for NCBI database search www.ncbi.nlm.nih.gov/gquery or a quiz where you’re only allowed to use PubMed to answer questions.

PubSearch & PubFetch allows users to “store literature, keyword, and gene information in a relational database, index the literature with keywords and gene names, and provide a Web user interface for annotating the genes from experimental data found in the associated literature” [11]

PubScience is either “peer-reviewed drinking” courtesy of pubsci.co.uk or an ambitious publishing project tragically axed by the U.S. Department of Energy (DoE). [12,13]

PubLick as far as I can see, hasn’t been used yet, unless you count this @publick on twitter. If anyone was launching a startup, working in the area of “licking” the tastiest data out of PubMed, that could be a great name for their data-mining business. Alternatively, it could be a catchy new nickname for PubMedCentral (PMC) or Europe PubMedCentral (EuropePMC) [15] – names which don’t exactly trip off the tongue. Since PMC is a free digital archive of publiclyaccessible full-text scholarly articles, PubLick seems like a appropriate moniker.

There’s probably lots more PubMed puns and portmanteaus out there just waiting to be used. Pubby, Pubsy, PubLican, Pubble, Pubbit, Publy, PubSoft, PubSort, PubBrawl, PubMatch, PubGames, PubGuide, PubWisdom, PubTalk, PubChat, PubShare, PubGrub, PubSnacks and PubLunch could all work. If you’ve know of any other decent (or dodgy) PubMed puns, leave them in the comments below and go and build a scientific twitterbot or cool tool using the same name — if you haven’t already.

Science and technology, especially bioinformatics, systems biology and the Web. It is a personal laboratory notebook-cum-diary, with a few facts and many opinions that would be difficult to publish conventionally [1].

2. What will you never write about?

Banal personal trivia (“I went shopping today”), confidential work, collaborative projects before they have been published. If in doubt, I try to ask people, “is it OK if I blog this?”

3. Have you ever considered leaving science?

Already did, I left science after my undergraduate degree to work in industry, but came back after six years to do a PhD. I don’t think Science ever really leaves you, once a scientist, always a scientist. Can’t see myself “leaving” again, but you never know.

I’ve been hunting all over the interweb looking for Professors that have blogs. While it would be a good thing if there were more, (see the science blogging challenge 2008), there are surprising amount of big boffins that already blog. I should say that by big, I mean (full) professor. By boffin I mean a person practicing science including biology, chemistry, physics, mathematics, engineering and hell, even computer “science” and the “dismal science” of economics too. By blog I mean, a web-log or a lab-log which is personal, frequently updated (with web feed) and allows comments. Here is my collection of big boffins with blogs, with a little help from friendfeed.com [1]. It is ordered alphabetically by surname and I hope it gives a flavour of some of the bloggers out there on the Web. If you know any more, please let me know. (more…)